From 98654da9b0d223400f7614192fb9f6845ba35d54 Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Fri, 21 Apr 2023 17:02:41 +0200
Subject: [PATCH] removed hub_penalty as parameter
---
cami_src/cami_suite.py | 20 +++++++++----------
.../seed_variation_script.py | 8 ++------
2 files changed, 12 insertions(+), 16 deletions(-)
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index 502ee9f..d41005f 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -245,7 +245,7 @@ class cami():
val_res_dct = set_validation_results['input_values']['values'][rel_score_name]
for val in val_res_dct:
f.write(f'{val}\t{val_res_dct[val]}\n')
-
+
# sub_validation_results = biodigest.single_validation.single_validation(
# tar=set(self.result_module_sets[result_set]),
# tar_id='entrez',
@@ -365,23 +365,23 @@ class cami():
'first_neighbours': cami_v1.make_first_neighbor_result_set}
}
- params_tr = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0],
- 'damping_factor': [0.1, 0.25, 0.5, 0.75],
+ params_tr = {'hub_penalty': [0.5],
+ 'damping_factor': [0.1, 0.25, 0.5, 0.75, 0.85],
'confidence_level': [0.2, 0.35, 0.5, 0.75],
'ranking': ['trustrank'],
'function': {'cami_v2': cami_v2.run_cami,
'cami_v3':cami_v3.run_cami}}
- params_b_m = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0],
- 'confidence_level': [0.2, 0.35, 0.5, 0.75],
- 'ranking': ['betweenness', 'harmonic'],
- 'function': {'cami_v2': cami_v2.run_cami,
- 'cami_v3':cami_v3.run_cami}}
+ # params_b_m = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0],
+ # 'confidence_level': [0.2, 0.35, 0.5, 0.75],
+ # 'ranking': ['betweenness', 'harmonic'],
+ # 'function': {'cami_v2': cami_v2.run_cami,
+ # 'cami_v3':cami_v3.run_cami}}
cami_setting_list = generate_param_combinations(params_0)+\
generate_param_combinations(params_1)+\
- generate_param_combinations(params_tr)+\
- generate_param_combinations(params_b_m)
+ generate_param_combinations(params_tr)#+\
+ #generate_param_combinations(params_b_m)
camis = {}
diff --git a/cami_src/evaluation_scripts/seed_variation_script.py b/cami_src/evaluation_scripts/seed_variation_script.py
index 5fdca37..be29a1d 100644
--- a/cami_src/evaluation_scripts/seed_variation_script.py
+++ b/cami_src/evaluation_scripts/seed_variation_script.py
@@ -55,7 +55,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
with open(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{cami.uid}_relevance_scores.tsv'), 'r') as f:
for line in f:
val_name = line.split('\t')[0]
- redisc_table.write(f'\t{val_name}')
+ res_table.write(f'\t{val_name}')
res_table.write('\n')
#result dictionaries of the form {tool:list(value for each iteration)}
@@ -87,11 +87,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
# reinitialize tools
cami.initialize_all_tools()
- # repeat consensus
- if ident%20==0:
- predict_and_make_consensus(cami)
- else:
- predict_and_make_consensus(cami)
+ predict_and_make_consensus(cami)
used_seeds = [cami.ppi_vertex2gene[seed] for seed in cami.seed_lst]
--
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